Category Archives: Streams

Amusing Monday: Using musical notes to describe salmon migration

Researchers working on innumerable scientific investigations throughout the world continue to present their findings in new and interesting ways, often apart from the usual charts and graphs. Some have turned to animation, others to interactive graphics and some to the medium of sound — a process called sonification.

Jens Hegg of the University of Idaho has collaborated with several musical composers to turn the migration of young chinook salmon into a musical score — although it doesn’t exactly have a beat you want to dance to.

In the first video on this page, you can close your eyes and imagine that you are standing at the mouth of the Snake River facing upstream, Jens advises in an email. To get the full effect, you need to listen with headphones. Fish moving on the Upper Snake River are represented by notes that sound the farthest away, the Clearwater River somewhat closer and the Lower Snake River closer still.

“The ocean is at your back, so as they enter the ocean, the washy sound sounds as if it is either behind you or directly between your ears,” Jens told me.

“Each river has it’s own set of tones that build a chord,” he continued. “The YouTube video uses the same WAV recording every time, but the actual sonification program randomly assigns fish to a new tone each time it is played, so that the music actually changes and is slightly different each time it is played while maintaining the same meaning.”

I have to confess that I’ve listened to this recording more than a dozen times and I’m still trying to visualize the movement in my mind. The map on the video actually helps with the understanding, but that’s not the movement of fish on the river that I’m trying to visualize. Jens said the program was set up so that fish in the Upper Snake are heard in the right ear; fish in the Lower Snake are heard in the left ear; and fish in the Clearwater are heard in the center.

Some sonification efforts result in music that is quite enjoyable to listen to. See Water Ways, Jan. 1, 2016. But if the point is to convey information, then the underlying music can sometimes be a distraction.

Jens told me that his experiments with sound originated in a roundabout way, somewhat out of desperation, as he tried to design his doctoral dissertation to meet the cross-disciplinary requirements for the program in Water Resources Science and Management.

“I had been told that the geology/ecology combination I had used for my master’s in the same program was not quite interdisciplinary enough, so I was in search of other possibilities,” he said.

Jens had read a newspaper profile about Jonathan Middleton of Eastern Washington University, who was creating music from protein data. He was finding that the people could discern variations in complex protein structure more easily with sonic rather than visual clues.

Jens always enjoyed music. He even writes his own songs. (See second video on this page.) Combining music and scientific data provided a fascinating challenge. “Nobody could say this wouldn’t be interdisciplinary,” he noted, “and it incorporates something I enjoy already, so it seemed like something worth pursuing.”

The data needed to create the sonic composition comes from Jens’ extensive study of salmon migration based on the ear bones of fish, called otoliths. Otoliths are composed of chemicals that build up over time as a fish grows. Rivers have their own chemical signatures, which are captured in the otoliths, so the movement of salmon can be determined by the chemical record stored in their ear bones.

Understanding the timing of salmon migration can help researchers figure out why some populations are more successful than others, especially as climate change shifts the timing of streamflows and alters the temperature and dissolved oxygen levels.

Mounds of otolith data were converted to notes with the help of Middleton at Eastern and Ben Luca Robertson at the University of Virginia. Middleton had developed a software program to help researchers turn their data into sound. Courtney Flatt of Northwest Public Broadcasting separated out some of the individual sounds in a piece she produced for Earthfix. Listen below.

      1. Tracking Salmon With Musical Notes

Part of Jens’ research was to see if people could tell when the sound pattern changed, thus discerning the movement of fish from one place to another. The complexity of the sound reduced the ability of listeners to distinguish transitions, according to a new report by Jens and his collaborators in the journal Heliyon. Check out the additional sounds and animations in the “supplementary content” at the end.

It also turned out that people were able to describe the changes more accurately if they were not watching a related animation. One reason could be that the visual clues caused people to divide their attention, focusing less on the sound.

“We have a long way to go before a sonification of a large number of fish can clearly indicate movement,” Jens told me in his email. “Our paper shows that people can accurately distinguish movement of individuals played alone, two at a time, or three at a time. But we haven’t spent as much time optimizing the sonification for a large number of fish.

“Knowing how it is set up helps in interpreting it,” he said. “On repeated listenings, you can hear times where larger numbers of fish are all moving at once from one place to another. These are the kinds of trends we want to highlight in terms of understanding salmon migration timing.”

Federal waters rule gets batted around endlessly in the courtrooms

Confusion is nothing new when it comes to figuring out whether federal agencies have jurisdiction over certain wetlands and intermittent streams under the Clean Water Act. And now the Trump administration has guaranteed that confusion will reign a while longer.

Meanwhile, lawsuits — also nothing new to the Clean Water Act, see how Babcock Partners can help here — continue to pile up at a rapid pace.

Some argue that the confusion begins with the 1972 Clean Water Act itself, which requires the U.S. Army Corps of Engineers to issue permits for any filling or dredging — which covers most development — within the “navigable waters” of the country.

Congress defined “navigable waters” in a way that has generated much confusion and many lawsuits through the years: “The term ‘navigable waters’ means the waters of the United States, including the territorial seas,” the law states.

Even the U.S. Supreme Court couldn’t figure it out and ended up adding to the confusion. In a 4-4-1 split ruling, half the justices focused on “navigable waters” with a narrow definition to include major waterways but avoid federal protection for many wetlands and intermittent streams. The other half of the justices supported a broader definition, which would protect downstream waters by also protecting upstream sources of water.

Writer Steve Zwick of Ecosystem Marketplace does a nice job explaining the legal and historical context for the confusion in a four-part series of articles. Zwick relies on, and gives credit to, the writings of William W. Sapp and William M. Lewis, Jr.

Under the previous administration of Barack Obama, the Army Corps of Engineers and the Environmental Protection Agency worked together to draft a new rule to more clearly define federal jurisdiction over streams and wetlands, as outlined by the broader Supreme Court opinion. It became known as the “Clean Water Rule” or “WOTUS” for Waters of the U.S.

Some potential opponents applauded the certainty of the proposed rule, even if they disagreed with some details. (See Water Ways, March 25, 2014.) But others believed that the states, not the federal government, should be in charge of protecting streams and wetlands. It became a common theme to argue that the new rule would regulate the tiniest ditches and farm ponds — something the Obama administration denied.

One of the opponents of the 2015 rule was Scott Pruitt, Oklahoma’s attorney general who ended up suing the Obama administration on behalf of his state. In all, 31 states joined various lawsuits against the rule, with separate lawsuits brought by farmers and industry.

Scott Pruitt, EPA administrator
Photo: EPA official portrait

“President Obama’s Environmental Protection Agency currently stands poised to strike the greatest blow to private property rights the modern era has seen,” Pruitt declared in an opinion piece co-authored by U.S. Sen. Rand Paul, a Republican from Kentucky. The piece was published in The Hill.

Pruitt, of course, is the man that President Trump later named to head the EPA, the same agency he was suing in multiple lawsuits. Pruitt said early on that he would not allow Obama’s WOTUS rule to go into effect.

Before it took effect, the WOTUS rule was tied up in the courts, including an injunction issued by the Sixth U.S. Circuit Court of Appeals in Cincinnati. Under the Clean Water Act, appeals courts can take primary action under certain conditions, but the U.S. Supreme Court agreed unanimously (PDF 923 kb) on Jan. 22 that the WOTUS rule is not one of these conditions.

And so the rule, originally scheduled to go into effect in August 2015, was put back into a confusing status, ready to go into effect in 37 states where it was not blocked by an injunction that covers 13 states under an order of the U.S. District Court in North Dakota.

“This is just all-out war. All-out litigation,” Vermont Law School professor Pat Parenteau was quoted as saying in an article by Ariel Wittenberg in E&E News. “This is good news for lawyers, but it is not going to be settled at all.”

Pruitt’s EPA then moved to finalize the Obama WOTUS rule on Jan. 31 but with an “applicability date” set for two years away. The announced intent was to overhaul the rule by pulling back federal jurisdiction over streams and wetlands.

“Today, EPA is taking action to reduce confusion and provide certainty to America’s farmers and ranchers,” Pruitt said in a news release. “The 2015 WOTUS rule developed by the Obama administration will not be applicable for the next two years, while we work through the process of providing long-term regulatory certainty across all 50 states about what waters are subject to federal regulation.”

In the interim, the EPA has announced that it will revert to previous policies and guidelines drafted following the confusing Supreme Court ruling.

You can guess what happened next. On Feb. 6, a total of 10 states, including Washington, plus Washington, D.C., filed a lawsuit in New York, claiming that Pruitt’s delaying tactics were illegal. The state officials, led by New York Attorney General Eric Schneiderman, argued that the federal government ignored the federal Administrative Procedures Act by adopting the revised rule without a meaningful comment period and in disregard of the Clean Water Act’s underlying intent of protecting the nation’s waters.

“The agencies have now suspended the Clean Water Rule without consideration of the extensive scientific record that supported it or the environmental and public health consequences of doing so,” the lawsuit (PDF 1.9 mb) says.

On the same day, the implementation delay was challenged in a separate lawsuit (2.6 mb) by two environmental groups, Natural Resources Defense Council and National Wildlife Federation.

“The Agencies’ only proffered rationale for the suspension is that it will promote regulatory clarity and certainty,” the lawsuit says. “In light of the administration’s open antipathy for the rule’s provisions, that rationale rings hollow. But it is also belied by the record. There is no evidence that suspending the rule will promote clarity or certainty, and ample evidence that suspending the Rule will create confusion and uncertainty.”

In Ariel Wittenberg’s story in E&E, Georgetown Law professor William Buzbee talks about how messy things have become.

“If the administration had taken the time to put out proposals that truly and fully engaged with the merits of the Clean Waters Rule and tried to come up with a new read, then it would be ordinary days in the courts,” he was quoted as saying. “But anything they do now, given their proposals, is likely to be legally vulnerable.”

Now the possibility exists that some courts could delay implementation of the original WOTUS rule while others reject the two-year delay. In any case, there is no end in sight to the legal battles, and nobody can be certain about what kind of projects will require federal permits.

Kitsap streams getting generally cleaner, but storms have an effect

Kitsap County’s streams are getting generally cleaner when it comes to bacterial levels, according to an annual water-quality report issued by the Kitsap Public Health District. But streams can have good years and bad years — and 2017 was not so good.

Let’s compare the annual report for 2016 to the newly released report for 2017, both found on the health district’s website. Reporter Tad Sooter offered a nice overview of the new report in a Kitsap Sun story on Friday.

Graph: Kitsap Public Health District

Before getting to the findings, it’s important to understand that there are two bacterial water-quality standards that must be met for a stream to get a clean bill of health. The first part calls for an average of no more than 100 bacteria per 100 milliliters of water (or no more than 50 bacteria if the water body has been designated “extraordinary”). The second part states that, regardless of the average, no more than 10 percent of the samples taken can exceed 200 bacteria per 100 milliliters of water (or 100 bacteria for “extraordinary” water).

It came as a surprise to me that in water year 2017 a total of 23 streams — or 35 percent of the 66 streams sampled — failed both water-quality standards. That’s worse than in water year 2016, when 25 percent of the 64 streams on the list failed both standards. (A water year goes from Oct. 1 to Sept. 30 of the next year.)

One reason that water quality got worse in 2017 was that rainy weather at times was more conducive to washing bacteria into the streams, according to Shawn Ultican, a water-quality expert with the health district.

“Bacterial levels were higher in general than we have seen them in the past few years,” Shawn said of the 2017 data. “We had more intense rainfall at times. We don’t think that suddenly more pollution sources have become a problem.”

Similar patterns also were seen in 2009 and 2010, he said.

More streams were deemed clean in 2016 than 2017. In 2017, 21 streams — 32 percent — met both of the water-quality standards, compared to 30 streams — 47 percent — the year before.

For discussion, I took a look at reports in 2008, when 38 percent met both standards, and 2013, when 29 percent met both standards. So it really does vary from year to year. And whether a stream is considered clean or polluted depends on recent rainfall and other fleeting factors. Consequently, much depends on when a water sample is taken, which is why health officials choose their sampling dates randomly.

Because weather plays an important factor in the bacterial counts, health officials tend to focus on long-term trends rather than on the results of individual water samples. Trends result from a statistical exercise using data collected each month over many years. For most streams, sampling has been going on for 22 years.

If the bacterial counts stay relatively the same over many years, the health of the stream is listed as “stationary.” If the numbers show a statistical trend, a stream will be listed as “worsening” or “improving.”

In 2017, five streams were listed as worsening: Coulter Creek in South Kitsap; Lofall and Kinman creeks in North Kitsap; and Stavis Creek and the Tahuya River, which drain into Hood Canal. You might consider Stavis Creek and Tahuya River to be statistical anomalies, because they are so clean that it takes only a few additional bacteria to result in an unwelcome trend.

Stavis Creek met both part 1 and 2 of the water quality standards in 2017, while the Tahuya River failed part 2 because of a few high counts. In 2016, both streams met both water-quality standards, so health officials aren’t worried about either stream at this point.

In 2016, 21 streams were listed as improving, compared to 18 streams in 2017. Olalla, Wilson, Barker and Chico creeks are among those that went from improving to stationary. Barker and Chico creeks are pretty clean, meeting both parts of the water-quality standards.

Tad’s story in the Kitsap Sun includes an interactive map that provides the status of each stream in Kitsap County monitored by the health district.

Lofall Creek, which includes drainage from the community of Lofall as well as upstream areas, has been giving health officials fits for years. Bacterial counts are high and getting worse, despite successful efforts to eliminate sources of pollution, such as failing septic systems and pet wastes.

Special tests are planned to see whether pollution in the stream is coming from pets, birds or ruminants, such as cows and deer, according to Ian Rork, an environmental health specialist with the health district who is assigned the cleanup of Lofall Creek and nearby Kinman Creek.

Health officials have long suspected that raccoons may be a source of the pollution, but they have no strong evidence. Raccoons are known to deposit their wastes in communal areas. As new development takes over uplands, these small animals may be pushed into remaining vegetated areas along the streams.

Last year, Ian began a new effort to work closely with residents of the community to see if they could take steps to discourage raccoons and other wildlife from congregating near Lofall. Steps people can take include making sure animals don’t have access to garbage, keeping barbecue grills clean and avoiding the intentional feeding of raccoons.

“The local residents have been so gracious and good to work with,” Ian told me, adding that most people are committed to solving the problem if only there were a clear answer.

For the 2017 report, Lofall Creek remains the most polluted stream in the county, followed by Ostrich Bay Creek in Bremerton; Olalla Creek and Burley Creek, both in South Kitsap; and Kinman Creek and Vinland Creek, both in North Kitsap.

The cleanest streams are Dewatto Creek, followed by Anderson Creek, Stavis Creek, Seabeck Creek, Salmonberry Creek, Big Beef Creek and Wright Creek. All drain into Hood Canal, except Anderson and Wright creeks, which drain into Sinclair Inlet, and South Kitsap’s Salmonberry Creek.

Climate change is expected to bring more intensive rainstorms, but how that will affect long-term trends in water quality is yet to be seen.

Amusing Monday: Amazing images through the magic of LIDAR

Spectacular images produced with the latest LIDAR technology ought to be considered works of art, at least in my humble opinion.

LIDAR software reveals current and historical stream channels for the Sauk River, a tributary of the Skagit.
Image: Washington State Geological Survey

The images on this page, which show geologic features in Washington state, were produced as part of a large-scale project to study the state’s geology. Funded by the Legislature in 2015, the project is largely designed to identify landslide hazards, but the LIDAR data has many wide-ranging uses for scientists, educators and political leaders.

Aside from LIDAR’s practical uses, I cannot get over how beautiful the images are, a feeling enhanced by the knowledge that the fine details reflect actual structures on the ground. All these images and 14 others are available as screensavers on the state’s LIDAR website.

At the Great Bend in Hood Canal, moving glaciers once carved out small hills, known as drumlins.
Image: Washington State Geological Survey

I asked Dan Coe, a GIS cartographer responsible for many of the final images, how much of an artist’s touch he uses when producing such amazing depictions of the landscape. Dan works for the Washington Geological Survey, a division of the Department of Natural Resources.

“There is definitely an artistic touch that is added to these images when they are produced,” he wrote in an email. “While each one is a bit different, depending on the landform featured, most follow a general process.”

LIDAR reveals changing stream channels where the Black and Chehalis rivers merge in Grays Harbor County. // Image: Washington State Geological Survey

LIDAR stands for light detection and ranging. When used from an airplane, LIDAR equipment shoots a laser beam along the ground. Sophisticated equipment and a computer interpret the reflected light as precise differences in elevation.

Dan blends the elevation data with other GIS layers provided by the software, including the outlines of landforms, shaded relief and water bodies.

“I then bring these layers into graphics software (usually Adobe Photoshop or Illustrator), where they are merged together,” Dan said. “This allows me to emphasize the features that are important to the viewer, usually with colorization and blending techniques.”

LIDAR reveals details of Devil’s Slide on Lummi Island in Whatcom County that cannot be seen otherwise.
Image: Washington State Geological Survey

The primary purpose of the images is to translate the science for a nontechnical audience, he said. That’s not to say that scientists don’t appreciate the effort, but the colorful images are somewhat simplified from the more detailed LIDAR data, he added.

“If done well, they are a good example of the ‘a picture is worth a thousand words’ adage,” he said, “and can go a long way to bridging the gap between science and public understanding.”

When it comes to his choice of colors, he acknowledges that he strives for a bit of a “wow!” factor, while enhancing the contrast “to draw the viewers eye and to emphasize the features more clearly.”

The video at right offers a good description of how LIDAR works. Early uses involved examining the topography and geology of an area with the trees stripped away. The surprising images revealed unknown features on the ground — including a piece of the Seattle fault at the south end of Bainbridge Island, where an earthquake raised Restoration Point about 20 feet some 1,100 years ago.

Since then, LIDAR has been refined for greater image resolution, and the improved software is providing new ways to interpret the data. For example, relative elevation models, or REMs, help to better visualize changes in river flows over time. The baseline elevation (0 feet) is defined as the surface of the river, so old river channels emerge as slight changes in elevation. Dan explains the REM process (PDF 16.5 mb) in a poster on the LIDAR website.

The mysterious Mima Mounds southwest of Olympia, as shown with LIDAR
Image: Washington State Geological Survey

The early use of LIDAR for revealing unseen geology has gradually given way to much broader applications. At first, the returning light that reflected off trees and vegetation was considered useless “noise” to be filtered out by computer. Later, scientists discovered that valuable information could be found within that noise — such as the size and type of trees and other vegetation growing in specific areas. These uses are explained in a video called “Introduction to Light Detection and Ranging.” Both videos mentioned in this blog post were produced by the National Ecological Observatory Network, or NEON, which is researching conditions and changes in ecosystems across the country.

A little-known lava flow, called West Crater, can be seen easily with LIDAR. The site is between Mount St. Helens and Mount Hood in Gifford Pinchot National Forest in Skamania County.
Image:Washington State Geological Survey

As Coe and his colleagues find new uses for LIDAR, they are also looking for new ways to encourage the public to understand the process and results. A nice two-page summary about the LIDAR program (PDF 2.6) can be found on the state’s LIDAR website. The website also includes descriptions of how LIDAR can be used in geology, forestry, graphics, navigation, meteorology and fire management, land-use planning, archeology and agriculture.

The page also includes an interactive story map called “The Bare Earth,” which takes you through various geological features. Interesting comparisons between LIDAR images and aerial photos of the same areas are shown in the story map.

Rains bring chum salmon back to their home streams

Salmon appear to be on the move in several local streams, thanks to the recent rains and increased streamflows. Wetter conditions no doubt triggered some of the migratory fish to head back to their spawning grounds.

A pair of chum salmon make it up Dickerson Creek, a tributary of Chico Creek. // Video: Jack Stanfill

It is still a little early in the season for coho and chum salmon to be fully involved in spawning activity, and there is plenty of time for people to get out and observe their amazing migration.

Salmon-watching is often a hit-or-miss situation, although Chico Creek is usually the best bet. After hearing several reports of chum moving upstream, I went out this afternoon to look in several local streams. Unfortunately, I did not get there before the rains stopped. What I saw in Chico Creek and other streams was fish milling about in deep pools, seemingly in no hurry to move upstream. Additional rains and streamflows are likely to get the fish fired up to move in and upstream more quickly.

Jack Stanfill, who lives on Dickerson Creek, a tributary of Chico Creek, said at least two adult chum reached his property today. Several restoration projects along Dickerson Creek probably helped the fish get upstream earlier than we have seen in previous years.

Jon Oleyar, who monitors the salmon migration for the Suquamish Tribe, told me that chum don’t normally get into Dickerson Creek until two weeks after they get into the upper reaches of Chico Creek. “This might be one of the earliest times ever,” Jon said.

As for other streams, the tribal biologist said he has seen early chum in Curley and Blackjack creeks in South Kitsap.

Viewing suggestions for this weekend:

  • Chico Creek: Chico Salmon Park (Facebook) along with a location just above the culvert under Golf Club Hill Road off Chico Way. Also check out the bridge near the 19th Hole Tavern on Erland Point Road and the access at the end of Kittyhawk Drive.
  • Dickerson Creek: Salmon Haven overlook on Taylor Road, off Northlake Way.
  • Curley Creek: Bridge on Southworth Drive near the intersection with Banner Road.
  • Blackjack Creek: A new bridge at Etta Turner Park between Port Orchard Ford and Westbay Center on Bay Street.
  • Gorst Creek: Otto Jarstad Park on Belfair Valley Road, where a new beaver dam has created a sizable pool of water, The dam may be limiting the migration of coho and perhaps blocking most of the chum.

Note for salmon-watchers: This year’s Kitsap Salmon Tours will be held in two weeks, on Saturday, Nov. 4. This year, the popular event has been expanded to seven locations. For details, go to the Kitsap WSU Extension website.

It appears that the chum coming into streams on the Kitsap Peninsula this year are noticeably larger in size than normal, perhaps in the 10- to 10.5-pound range, Jon Oleyar told me. That exceeds the normal 8- to 10-pound size for chum, he said.

Orca Network reported today that some of our Southern Resident killer whales have been foraging this week off the Kitsap Peninsula as well as in other areas not easily identified because of the dark, stormy weather we have had. Let’s hope the orcas can find enough food to stick around awhile.

On Sunday, a small group of whales from L pod showed up in the San Juan Islands for the first time this year. Normally, these whales — L-54 and her offspring along with males L-84 and L-88 — would be seen numerous times during the summer, but this was a highly unusually year. They were seen this week with J pod, which hasn’t been around much either.

On Monday, reports of orcas near Kingston and Edmonds suggested that the whales had moved south. They were later spotted near Seattle and then again near Kingston on Tuesday, when they headed out of Puget Sound by evening.

It is often said that the orcas will go where the salmon are. They are known to prefer chinook when their favorite fish are available, but they will switch to chum after the chinook run is over. It will be interesting to how much time the whales spend in Central and South Puget Sound, where chum are more plentiful.

The total number of chum salmon predicted this year — including those harvested along the way — is expected to be lower than last year. Still, there is hope that the preseason forecast will be exceeded by the actual return. The total predicted for Central and South Puget Sound is 433,000 chum, with 85 percent returning to streams and 15 percent coming back to hatcheries.

Last year, the total predicted run was 526,000 chum, about 21 percent higher than this year. Typically, the number of chum returning in odd-numbered years is lower than in even-numbered years, other things being equal. That’s because odd-numbered years is when the vast majority of pink salmon spawn, resulting in increased competition and lower survival for the young chum. Smaller numbers of juveniles mean fewer adult chum that return four years later during another odd-numbered year, continuing the cycle.

Most of the difference between last year’s and this year’s chum run can be accounted for in the odd- versus even-numbered years, said Aaron Default of the Washington Department of Fish and Wildlife.

It is too early in the season to update the preseason forecast based on commercial and tribal fishing that has taken place so far, Aaron said. As usual, fishing seasons are likely to be adjusted up or down when more information becomes available. The main goal is to make sure that enough fish make it back to sustain and potentially increase the salmon population.

Amusing Monday: celebrating the nation’s wild and scenic rivers

The value and enjoyment of rivers throughout the United States will be highlighted over the next year, as the Wild and Scenic Rivers Act approaches its 50th anniversary on Oct. 2, 2018.

Some 12,700 miles of rushing waters are protected on 208 rivers designated in 40 states plus the Commonwealth of Puerto Rico. A Wild and Scenic River designation is the strongest protection for rivers in our country, safeguarding clean water, recreation, fish and wildlife, and cultural heritage, according to American Rivers, an environmental group focused on river protection. Check out the webpage “Why do we need wild rivers?”

“Free-flowing rivers create natural riparian areas that foster healthy, abundant, and diverse wildlife and are the centerpieces of rich ecological processes,” according to a news release from the National Parks Service. “Recreationally, free-flowing rivers offer unparalleled inspirational experiences from challenging whitewater to placid fishing. Through the arterial connections of rivers to communities, we all live downstream of a Wild and Scenic River.”

The first video on this page, called “Make Your Splash,” celebrates a family enjoying water recreation. It was produced by the Park Service in conjunction with three other federal agencies and several nonprofit organizations.

To call attention to the importance of wild rivers, American Rivers has launched a program called “5,000 Miles of Wild” with the goal of putting an additional 5,000 miles of wild rivers into protected status.

As part of the effort, the organization is working to collect 5,000 stories from people around the country who have a place in their hearts for special rivers, as explained in “About the campaign.” The second video, “5,000 miles of wild,” promotes the campaign.

I think you will enjoy the personal stories about rivers and the photos submitted to the page “My River Story.”

I would like to see more submissions from people in Washington state, because we have some of the most beautiful and productive rivers in the U.S., and I know there are many personal connections to these special places. Among the Washington folks submitting stories is Paul Cain of Bow, who applauds the efforts of state fish and wildlife officers in an encounter along Samish River in North Puget Sound. Also, Peggy File talks about growing up on the Skagit River, one of the rivers designated wild and scenic.

Former President Jimmy Carter offers a testimonial about taking his own life into his hands on the Chattooga River, which flows from North Carolina into Georgia. The powerful river, he said, “kind of opened my eyes to a relationship between a human being and a wild river that I had never contemplated before.”

As president, Carter said he vetoed about 16 different dam projects throughout the country, because he believed they were counterproductive to the well-being of Americans.

American Rivers has compiled a list of rivers that warrant protection on its page “What is the 5,000 Miles of Wild campaign?” In Washington, protections are proposed for 688 miles of rivers in the North Cascades, including the Nooksack River, and 454 miles of rivers in the Olympic Mountains (Wild Olympics Campaign).

Fiftieth anniversary water bottle, Cafe Press

For existing wild and scenic rivers, take a look at the U.S. map or the map of Washington state. Other information is compiled on a government website called “National Wild and Scenic Rivers System.” The website also has a page with information about the 50th anniversary celebration. One can even purchase a variety of clothing and products showing off the 50th anniversary logo from Cafe Press.

An audio project by American Rivers was composed by intern Annemarie Lewis, who worked this past summer in the Colorado River Basin. She talks about culture, history and science of rivers, as related by a variety of people closely connected to this issue. The project is called “We are rivers: Conversations about the rivers that connect us.”

Speaking of American Rivers projects, I got a kick out of a video completed in 2015 called “50 Favorite Things We Love about Rivers.” See Water Ways, Feb. 23, 2015.

Carpenter Creek culvert is gone, as bridge work pushes to meet schedule

UPDATE, Thursday Oct. 26

The bridge construction will continue beyond the end of the year, when it was originally scheduled for completion. The new completion date is listed as March 2018.

“The delay is due to numerous issues and challenges, including encountering old buried wooden pilings and associated contaminated material, a revised sanitary sewer design, and labor and materials shortages, which disrupted the construction schedule,” according to a news release from Kitsap County. “The onset of the winter weather months will also add to the delay as final work on the project, such as paving, depends on fair weather.”
—–

An old five-foot culvert where Carpenter Creek passes under West Kingston Road is now down to its last bit of concrete plus a wedge dirt, with final removal awaiting completion of a new 150-foot-long bridge.

Only one section of the old culvert remains on Carpenter Creek after other pieces were pulled out two weeks ago. // Photo: Sillwaters Environmental Center

Massive amounts of earthen fill and have been removed since the project started about six months ago. All that remains is the wedge of dirt that still supports pipes and utilities, which will be attached to the bridge during construction. After that, the last fill material will be removed, leaving a wide-open estuary flowing under the bridge.

The construction has created some inconvenience for folks in the Kingston area, but the project promises to enhance salmon migration in Carpenter Creek, restore tidal function in the estuary and enhance the salt marsh for a variety of creatures. The creek and/or the estuary may be used by chum, coho and chinook salmon, along with steelhead and cutthroat trout.

Stillwaters Environmental Center is coordinating monitoring in the estuary to measure improvements in the ecosystem. Before and after elevation measurements will help describe the physical changes, while biological surveys identify changes in water quality, vegetation, fish and insect populations, among other things.

A new bridge takes shape where West Kingston Road crosses the upper estuary of Carpenter Creek. // Photo: Kitsap County Public Works

I am particularly interested in how the new bridge will further improve the function of the estuary, which is the last major stop-over point for juvenile salmon on their way out of Puget Sound, according to biologists. The bridge on West Kingston Road is the second phase of a project that began in 2012, when a small box culvert was replaced with a 90-foot-long bridge on South Kingston Road. The first bridge crosses the lower estuary, while the new bridge crosses the upper estuary.

While my focus has been on life in the estuary, the project goes beyond the ecosystem, Kitsap County Commissioner Rob Gelder told Kitsap Sun reporter (now retired) Ed Friedrich in a story published in March at the beginning of construction.

Here’s what the old culvert looked like before the recent project began.
Photo: Kitsap County Public Works.

“This isn’t just a culvert-replacement project but a project that will increase the safety and functionality for drivers and pedestrians alike,” Rob said. “Road closure is never easy, but I hope the community will appreciate the improvements when it’s all complete.”

The work involves widening the travel lanes, adding 5-foot pedestrian and bike lanes on the north side and a 6-foot paved shoulder on the south side. In addition, street lighting will be added.

As of today, the project has fallen behind schedule, according to Tina Nelson, senior program manager for Kitsap County Public Works. Tina said she hopes the contractor, Redside Construction of Bainbridge Island, will catch up enough to allow the road to reopen by the end of December, as originally scheduled.

Officials will be assessing the situation through the end of October, she said. If it appears the bridge and roadway won’t be ready for opening by Dec. 31, then an announcement will be made in late October or early November. Advance notice is needed because of school bus routing and scheduling after the new year.

The causes of the delay are many, Tina told me, but it generally boils down to scheduling of project materials and crews, for which the contractor is responsible. The contract calls for the work to be done in a certain number of days, she said, and the contractor will lose money if the work is not completed on time.

So far, fish passage has not been an issue, although chum salmon could soon move into the estuary — if they haven’t already — as they begin their fall migration. If fish try to move upstream before the channel is reopened, officials with the Washington Department of Fish and Wildlife will help determine the best way to safely get them upstream.

Much of the $3-million project is funded by the Navy as mitigation for ecological damage caused by the 2012 renovation of Pier B at Naval Base Kitsap-Bremerton.

Are we winning or losing the ongoing battle for salmon habitat?

It has been said that the Puget Sound ecosystem would be far worse off today were it not for the millions of dollars spent on restoration projects over the past 25 years.

Undoubtedly, that’s true, but I think most of us are hoping that these costly efforts will eventually restore salmon populations while improving conditions for other creatures as well. Shouldn’t we be able to measure the progress?

Juvenile chinook salmon
Photo: John McMillan, NOAA

This basic question became the essence of my latest story published in the Encyclopedia of Puget Sound: “Are we making progress on salmon revovery?”

As I describe in the story, what seems like a simple question becomes tangled in the difficulties of measuring population and ecological changes. It turns out that you can’t just count the fish to see if restoration is working. That’s because natural variabilities of weather, ocean conditions and predator/prey populations cause salmon populations to swing wildly from year to year no matter what you do.

While researching this story, I learned a good deal about freshwater habitat conditions needed to help various species of salmon to thrive. Habitat improvements resulting from restoration projects are no doubt helping salmon in significant ways. On the other hand, one cannot ignore human development that continues to degrade habitat — despite improved regulations designed to reduce the damage.

I’ve heard some people say that wild salmon would come back in larger numbers if everyone would just stop fishing for them. This may be true to some extent, especially for high-quality streams that may not be getting enough salmon to spawn. But the key to the problem is understanding the “bottlenecks” that limit salmon survival through their entire lives.

A stream may have plenty of adult spawners, but that does not mean the salmon runs will increase if the eggs are buried in silt or if food supplies limit the number of fry that survive. There may be multiple limiting factors that need to be addressed to ensure healthy ongoing salmon populations.

Small improvements in habitat may actually boost the productivity of salmon in a stream, meaning that more salmon will survive. But the benefits of small projects on large streams may be difficult to distinguish from natural variation. Statistical analysis is used to determine whether increases or decreases in salmon populations are more related to habitat changes or natural variation. It takes a fairly dramatic change to link cause to effect in a statistically significant way.

One ongoing experiment is measuring changes in fry populations in several streams within the same watersheds. One stream is left alone — the “control” stream — while habitat improvements are made in others. Because the streams are closely related, biologists hope to attribute population increases to habitat improvements with a high level of certainty. See Intensively Monitored Watersheds on the website of the Washington Department of Fish and Wildlife.

The same issue of statistics applies to the aquatic insects that salmon eat. It appears that food supplies are improving in many salmon streams as a result of restoration, but not all benthic invertebrates are responding in the same way. For many streams, it will take more time to get enough data to determine whether the increased bug populations are statistically significant. This happens to be one issue that I side-stepped in the latest story, but I will be returning to it in the future. For background, check out an earlier story I wrote for the Encyclopedia of Puget Sound, “Healthy Streams, Healthy Bugs.”

While habitat restoration is ongoing, so too is human development, which continues unabated at what appears to be an accelerating pace. New regulations are designed to result in “no net loss” of important habitats, including shorelines, streams and wetlands. But questions remain about whether local regulations themselves and/or enforcement of the regulations are adequate.

Biologists at NOAA’s Northwest Fisheries Science Center are conducting research to determine whether habitat changes are for better or worse, especially with regard to chinook. We should see some results within the next few years, as the agency prepares to draft the next five-year status report for Puget Sound’s threatened chinook population.

Winter chum salmon in South Puget Sound fail test for uniqueness

Sam Wright, who has been remarkably successful in getting various fish species protected under the Endangered Species Act, has learned that his latest ESA petition — possibly his final petition — has been rejected.

Sam, who retired from the Washington Department of Fish and Wildlife after years of studying salmon and other fish, would like to get special recognition for a unique population of chum salmon that return to South Puget Sound in the winter.

Nisqually River near Interstate 5 bridge
Photo: ©2006 Walter Siegmund/Wikimedia Commons

The Nisqually-Chambers Creek run of winter chum is the only population of chum salmon in the world that spawn as late as February, with some fish entirely missing the worst floods of December and January, Sam told me. His petition to the federal government was designed to get these winter chum recognized as a distinct population segment — much as the threatened summer chum population in Hood Canal has been designated as separate from the fall runs of chum throughout Puget Sound.

Being a small population, the Nisqually-Chambers Creek winter chum would probably qualify for threatened or endangered status, he said, but first it would need to be recognized as distinct. If not listed initially as threatened or endangered, those decisions could follow if the population crashes, he said.

“The petition was meant to correct what was, from my perspective, a mistake made 20 years ago when they made a coastwise series of reports assessing the chum salmon populations,” said Sam, who is now 81 years old.

“In the entire range of chum salmon — both in North America and Asia — there are 3,500 streams with chum salmon,” he continued, “but there is only one single winter-run chum salmon, and that is the Nisqually.”

Sam’s petition (PDF 4.2 mb), filed more than two years ago, was subject to a 90-day review by the National Marine Fisheries Service, also known as NOAA Fisheries. Sam was told that the petition had been misplaced all this time. Last week, he got the news that the Nisqually-Chambers Creek winter chum would not be recognized as a distinct population, nor would it be considered for further review without new information being brought forward.

In rejecting Sam’s petition, NOAA’s Northwest Fisheries Science Center reviewed available data — including a 2015 genetic study on chum populations — and concluded that the original analysis done in 1997 was still valid. That analysis concluded that the winter-run chum are closely related to the fall-run chum in Puget Sound and Hood Canal and that “there is no clear genetic evidence to support the idea that the winter-run chum salmon in Puget Sound are substantially reproductively isolated from other chum salmon populations in southern Puget Sound.” See “Listing Endangered or Threatened Species …”

Sam argues that the winter chum remain genetically isolated from fall chum populations because of their unusual spawning schedule. That is demonstrated by annual population counts, which go up and down independently of fall chum numbers in South Puget Sound.

“They are reacting to different environmental conditions,” Sam explained.

Studies are needed to show the differences, Sam said, but they may have an advantage over fall chum by avoiding most of the winter floods, which can displace salmon eggs incubating in the gravel or else smother them in silt.

Incubation time is based on temperature, so the late-arriving chum are subject to warmer water and faster incubation. The winter chum fry are only a little behind the fall chum fry, Sam said.

One of the most productive areas for winter chum is Muck Creek, a tributary of the Nisqually River that runs through Joint Base Lewis McCord, where the Army conducts military exercises, according to Sam.

“We’ve had decades of battles with Fort Lewis over whether to use Muck Creek as part of their firing range,” Sam told me, adding that he suspects that pressure from the military played a role in NOAA’s original decision to lump the winter chum together with the fall chum.

Personally, I don’t know anything about such conflicts, but Muck Creek has been the site of a major restoration effort involving JBLM, the Nisqually Tribe and other groups. In 2011, reporter Ingrid Barrentine wrote about the annual salmon homecoming for Northwest Guardian, a JBLM publication.

As for the habitat in Muck Creek, Sam told me something else that was surprising. The stream is spring-fed with freshwater bubbling up from below and providing stable flows, he said. That helps the eggs to survive. Unlike many streams in which only 10 percent of the chum eggs grow into fry headed for saltwater, Muck Creek has had a 90-percent survival rate.

One reason that Sam is so concerned about the Nisqually-Chambers Creek winter chum is the uncertainty about what is coming in the future. Climate change is likely to bring higher stream flows in winter, he said, and chum runs that come later may hold the keys to survival of the species.

“To me, the last thing we want to do is throw away that particular piece,” Sam said, paraphrasing Aldo Leopold, whose exact quote is this:

“If the biota, in the course of aeons, has built something we like but do not understand, then who but a fool would discard seemingly useless parts? To keep every cog and wheel is the first precaution of intelligent tinkering.” (Round River)

Sam Wright’s persistence has paid off in the past when he has asked for reconsideration and finally received threatened or endangered status for various populations of salmon, steelhead, rockfish and other marine species. This time, he may or may not provide additional information and ask the agency to reconsider its position. In any case, Sam told me that he has no new petitions in the works, and this may be his last effort.

Whether Nisqually-Chambers Creek winter chum — or any salmon population — is considered distinct rests on NOAA’s definition of species, 16 U.S.C. 1531, which includes two criteria:

  1. The population must be substantially reproductively isolated from other nonspecific population units; and
  2. The population must represent an important component in the evolutionary legacy of the species.

In turning down Sam’s petition, reviewers pointed to genetic studies that supported the finding that summer chum in Hood Canal and the Strait of Juan de Fuca were distinct from other chum runs. A second grouping included the remaining fall, summer and winter runs in Puget Sound, with a third grouping of fall chum from the Strait of Juan de Fuca, the Washington Coast and Oregon.

The reviewers also pointed out that the Nisqually River and Chambers Creek to the north are not geographically isolated from the rest of South Puget Sound.

As for “evolutionary legacy,” Sam contends that loss of the winter chum would be forever, as with extinct summer chum in many river systems including Chambers Creek. That critical issue, he said, is the very definition of legacy.

The reviewers of his petition found, like the 1997 review team, that winter and summer runs in Puget Sound only showed “patterns of diversity within a relatively large and complex evolutionarily significant unit,” known as an ESU.

“Both the Nisqually River and Chambers Creek watersheds have supported both summer- and fall-run chum salmon in the past, along with winter-run chum salmon,” concluded the agency’s written findings, “so there is nothing unique preventing these watersheds from supporting multiple chum salmon runs.”

Forest battle continues over defining the upper bounds of fish habitat

A long-running battle over how to manage potential fish habitat on commercial forestland could be coming to a head — although it isn’t clear if the solution will satisfy either forestland owners or environmentalists.

Jamie Glasgow of Wild Fish Conservancy (center) leads a crew surveying a stream for the presence of fish in 2014. // Photo: Chris Linder

To be clear, there is not much argument about streamside buffers where salmon, trout and other fish are readily found, thanks to state and federal rules stemming from the landmark Forests and Fish Report. Buffers are designed to save trees that serve the needs of fish — including insects for food, shade for cool water and eventually down trees that form pools for resting as well as hiding places and spawning areas.

Environmentalists contend that it is important to protect unoccupied fish habitat as well as areas occupied by fish at any point in time. If salmon populations are to rebound, salmon fry could need extra space to grow and develop, says Jamie Glasgow, a biologist with Wild Fish Conservancy. That means larger buffers should go where fish habitat can be found.

Of course, timberland owners don’t want to leave large buffers on small stream segments where fish would never go. For them, perhaps hundreds of millions of dollars in commercial timber could be left standing under new rules, depending on how the state’s Forest Practices Board comes down on this issue of fish habitat. The board is scheduled to take up the issue again with some kind of action planned on Aug. 9.

Fish habitat is defined in the Forest and Fish Report as areas of a stream “used by fish at any life stage at any time of the year, including potential habitat likely to be used by fish which could be recovered by restoration or management and includes off-channel habitat.” (The emphasis is mine.)

The Forest and Fish Report was incorporated into state law by the Washington Legislature, and federal agencies adopted those concepts as a statewide “habitat conservation plan” to protect species listed under the Endangered Species Act, including chinook salmon.

One of the big arguments about fish habitat revolves around how to determine just how far upstream fish would likely go and where they would be deterred under various natural conditions they encounter, such as streamflow or natural barriers such as waterfalls.

The Forest and Fish Report anticipated that a map would be developed with all stream segments designated as either fish habitat or not fish habitat. After several years, such a map was developed in 2005, based on the size and steepness of the streams, using the best information available.

It soon became apparent, however, that fish were being found in areas marked as non-habitat on the maps. Other areas designated as habitat were sometimes unable to support fish. Some fish-bearing streams were not even on the maps, and some streams were in the wrong place. I wrote about the efforts by Wild Fish Conservancy to correct some maps three years ago (Kitsap Sun, Sept. 27, 2014). Previous maps had proved to be a problem as well, even before the Forest and Fish Report (Kitsap Sun, May 28, 1996).

The maps are still used as guidance, but buffer determinations must be made for each logging or development project based on actual site conditions. If a stream is 2 feet wide and the steepness is less than a 20 percent — or 16 percent in some areas — it is assumed that fish can get there.

But — and here’s the rub — an allowable fall-back method is to identify the presence of fish, either through snorkel surveys or by “elecrtrofishing,” which involves putting a nonlethal current in the water to stun the fish. Where fish are located, the area is designated as fish habitat, along with waters that extend upstream to a natural “break,” such as a waterfall or a stream confluence that would prevent fish from going any farther.

Much history surrounds this issue, and all sides should be given credit for working through many thorny habitat problems through the years. Nobody wants to go back to a time when the spotted owl was a symbol for conflict about whether forests were mainly for jobs or fish and wildlife.

As for fish habitat, experts have renewed their attempt to come up with reliable and objective methods to identify the break points between habitat (known as “Type F waters,” which stands for fish) and non-habitat (“Type N waters”) without the costs and impacts of surveying every stream for fish.

Environmental groups became impatient with the effort — or lack of effort at times — over the past 12 years — or more if you go back to the Forest and Fish Report. The matter has gone into formal dispute resolution, as provided by the Forest and Fish Law, and it now is up to the Forest Practices Board to provide a resolution.

“For the past 12 years, we have been using the interim water-typing rule that does not protect fish habitat …,” Glasgow said. “The interim rule allows surveyors to go to a stream anytime (during a specified period) and electrofish a stream. If they do not find fish during the one-day survey, they can identify it as Type N.”

The result is that many miles of fish habitat are getting little or no buffer protection, he argues. Where mistakes are made and small buffers or no buffers are allowed, it will take decades before the trees grow back to become good habitat again.

In mediation talks, the various parties — landowners, environmental groups, tribes and governments — have come to consensus on the overall framework to identify break points where the fish habitat ends, but the details are still unresolved.

Karen Terwilliger, senior director of forest and environmental policy for the Washington Forest Protection Association, said it is important to remember that these discussions are not about streams where adult salmon will go to lay their eggs.

“It’s the tail end of where the fish might be,” said Terwilliger, whose organization represents large timberland owners. The areas in dispute are generally small streams mostly occupied today by resident fish, including various species of trout and tiny sculpins.

The break point between fish and non-fish areas should be a location where the last fish is equally likely to stop above and below that point, she said. The scientific standard is that the break point should be accurate 95 percent of the time, as required by adaptive management provisions of the Forest and Fish Law.

“We think fish presence will always be an important part of the system,” she said. “Different streams are different. A ‘one size fits all’ does not make sense.”

Environmental groups prefer to avoid methods that rely upon people finding fish, which may or may not be present at the time of a survey. It should be possible to define habitat conditions suitable for fish whether or not they are there at a given time.

Scientific information has evolved to where predictions can be made about where fish will go, Terwilliger said, but there are still questions about what conditions create a barrier to fish. A level of scientific certainty is required before changes can go forward.

“If science says a change needs to be made, then you more forward to make the change,” she said. “To date, we have not seen data that a lot of changes need to be made.”

If a rule change is proposed, it will need to undergo environmental review, a cost-benefit analysis, a small-business economic impact statement and public hearings.

Peter Goldman, director and managing attorney at Washington Forest Law Center, said the adaptive management process should be more than a system of delays. Only recently have things been moving in the right direction, he added.

“The timber industry is powerful,” said Goldman, who represents environmental groups. “They don’t want anything to change.

“We have been trying to negotiate in good faith collaboratively, because that is the Washington way,” he said. “If the Forest Practices Board doesn’t act … it is conceivable that we will have to sue the board and ask the federal government to reconsider the HCP.”

Stephen Bernath, deputy supervisor for forest practices at the Washington Department of Natural Resources and chairman of Forest Practices Board, said the board is moving forward with the help of scientists. New ideas and new technology are being brought into the discussion with the goal of seeing whether a variety of physical parameters alone can be used to identify fish habitat with high probability.

At the Aug. 9 meeting, the board is scheduled to get an update on the progress and to act on staff recommendations about the breaks between fish and non-fish waters. After that, a formal process will begin to incorporate changes into policies, rules and guidance.